Re: [gmx-users] Re: Problem calculating RMSD with gromos

2013-07-02 Thread Justin Lemkul
On Tue, Jul 2, 2013 at 10:51 AM, Melchor S. wrote: > Hi Tsjerk, > > I read the sae that you say about the PME and the twin cutoff, but as I > have seen that a lot of studies in that people use Gromos with PME and a > Vander Vaals cutoff so small as mine, I didn't change it, for mantain the > sam

Re: [gmx-users] Re: Problem calculating RMSD with gromos

2013-07-02 Thread Tsjerk Wassenaar
Hi Melchor, Have you looked at the structures? The GROMOS people suggest using twin-range cut-off with reaction field correction, and the Vanderwaals cutoff you use seems a bit small, as 1.4 nm is commonly used with GROMOS. Maybe that makes a difference. Cheers, Tsjerk On Tue, Jul 2, 2013 at 3